GeneralTop ↑
The atlas system has two main elements:
- An illustrated text describing 18 hippocampal structures and 63 boundaries between these structures. The structure descriptions can be accessed from an alphabetical or hierarchical index.
- An image repository of ~100 coronal images showing the cyto- and chemoarchitecture of the hippocampus region. The images are organized in triplets of neighbouring sections stained for calbinding, NeuN, and parvalbumin. The image triples are sorted from anterior to posterior by distance from bregma.
The structure and boundary definitions and the image viewer open in separate browser windows, and bidirectional links are provided between corresponding structure descriptions and image levels. Tools for querying are not yet implemented. For optimal use it is recommended to view the browser windows in full screen, preferably using a dual screen setup.
Index of structuresTop ↑
To use the index of structures, scroll through the alphabetical or hierachical index to a structure name of interest. Links are provided to structure and boundary descriptions as well as to corresponding levels in the image repository.
The structure descriptions give a review of key anatomical features, and provides links to descriptions of boundaries with surrounding structures and corresponding levels in the image repository.
The boundary descriptions review the characteristic histological criteria used to identify the boundaries in histological sections, together with links to corresponding levels in the image repository.
Image viewerTop ↑
To use the image viewer first drag the slider under the row of thumbnail images horizontally to select an anterioposterior level of interest (Bregma coordinates are indicated). Click on the thumbnail images to open them in the triple viewer. The image panels show images of sections stained for calbindin (left), NeuN (middle), and parvalbumin (right). Not all image triplets are complete.
The viewer has the following options for navigating the images:
- Zoom, click the + button in the toolbar or press the shift key to zoom in; click the - button or press the ctrl key to zoom out
- Pan, click the arrows in the tool bar, or left-click and drag the images freely in the viewer
- Synchronize, to synchronize the three viewer panels to the same position and zoom scale, click the = button in the toolbar
- Pre-set, to navigate to a predefined view of a given region, select a structure in the Annotation toolbar and click GO
- Reset, to reset viewer to default, click the reset button in the toolbar
- Annotation, click the annotation button in the toolbar to toggle annotations on and off. Graphical overlay is only available for the NeuN images in the middle viewer panel. The employed color coding is in correspondence with the interactive connectivity diagram provided by van Strien et al., 2009; Nat Rev Neurosci.10:272-282
- Scale bar, the ZoomScale bar shows a scale bare for the image panels. The bar is transparent and can be moved to make crude measurements in the images
To look up structure descriptions and boundary definitions, click on the color-coded structure name abbreviations in the top panel.
Examples of use: Top ↑
The atlas system is designed to provide both text description and annotated histological details from the rat hippocampus. The atlas has two main elements, which serve as entry points for use:
- Find a structure of interest using the alphabetical or hierarchical structure index
- Find a structure or position of interest using the image repository and the provided stereotaxic positions (bregma levels).
A student of the hippocampal region may for example use the structure index as a starting point to read about the structure, and then explore the histoarchitecture in the image repository.
A researcher seeking to define a boundary in experimental histological material, may for example look up a corresponding level in the image repository, and then read about boundary definitions through the index of structures.
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